Tuber on a chip: differential gene expression during potato tuber development

B.A. Kloosterman, O.F.J. Vorst, R.D. Hall, R.G.F. Visser, C.W.B. Bachem

Research output: Contribution to journalArticleAcademicpeer-review

71 Citations (Scopus)

Abstract

Potato tuber development has proven to be a valuable model system for studying underground sink organ formation. Research on this topic has led to the identification of many genes involved in this complex process and has aided in the unravelling of the mechanisms underlying starch synthesis. However, less attention has been paid to the biochemical pathways of other important metabolites or to the changing metabolic fluxes occurring during potato tuber development. In this paper, we describe the construction of a potato complementary DNA (cDNA) microarray specifically designed for genes involved in processes related to tuber development and tuber quality traits. We present expression profiles of 1315 cDNAs during tuber development where the predominant profiles were strong up- and down-regulation. Gene expression profiles showing transient increases or decreases were less abundantly represented and followed more moderate changes, mainly during tuber initiation. In addition to the confirmation of gene expression patterns during tuber development, many novel differentially expressed genes were identified and are considered as candidate genes for direct involvement in potato tuber development. A detailed analysis of starch metabolism genes provided a unique overview of expression changes during tuber development. Characteristic expression profiles were often clearly different between gene family members. A link between differential gene expression during tuber development and potato tissue specificity is described. This dataset provides a firm basis for the identification of key regulatory genes in a number of metabolic pathways that may provide researchers with new tools to achieve breeding goals for use in industrial applications.
Original languageEnglish
Pages (from-to)505-519
JournalPlant Biotechnology Journal
Volume3
DOIs
Publication statusPublished - 2005

Fingerprint

Solanum tuberosum
tubers
potatoes
Gene Expression
gene expression
Genes
Starch
Complementary DNA
genes
Organ Specificity
biochemical pathways
Regulator Genes
Metabolic Networks and Pathways
Oligonucleotide Array Sequence Analysis
Transcriptome
Breeding
starch
Up-Regulation
Down-Regulation
taxonomic keys

Keywords

  • solanum-tuberosum
  • phytochrome-b
  • gibberellin 2-oxidases
  • sucrose
  • starch
  • tuberization
  • plants
  • fructokinase
  • photoperiod
  • conversion

Cite this

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title = "Tuber on a chip: differential gene expression during potato tuber development",
abstract = "Potato tuber development has proven to be a valuable model system for studying underground sink organ formation. Research on this topic has led to the identification of many genes involved in this complex process and has aided in the unravelling of the mechanisms underlying starch synthesis. However, less attention has been paid to the biochemical pathways of other important metabolites or to the changing metabolic fluxes occurring during potato tuber development. In this paper, we describe the construction of a potato complementary DNA (cDNA) microarray specifically designed for genes involved in processes related to tuber development and tuber quality traits. We present expression profiles of 1315 cDNAs during tuber development where the predominant profiles were strong up- and down-regulation. Gene expression profiles showing transient increases or decreases were less abundantly represented and followed more moderate changes, mainly during tuber initiation. In addition to the confirmation of gene expression patterns during tuber development, many novel differentially expressed genes were identified and are considered as candidate genes for direct involvement in potato tuber development. A detailed analysis of starch metabolism genes provided a unique overview of expression changes during tuber development. Characteristic expression profiles were often clearly different between gene family members. A link between differential gene expression during tuber development and potato tissue specificity is described. This dataset provides a firm basis for the identification of key regulatory genes in a number of metabolic pathways that may provide researchers with new tools to achieve breeding goals for use in industrial applications.",
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Tuber on a chip: differential gene expression during potato tuber development. / Kloosterman, B.A.; Vorst, O.F.J.; Hall, R.D.; Visser, R.G.F.; Bachem, C.W.B.

In: Plant Biotechnology Journal, Vol. 3, 2005, p. 505-519.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Tuber on a chip: differential gene expression during potato tuber development

AU - Kloosterman, B.A.

AU - Vorst, O.F.J.

AU - Hall, R.D.

AU - Visser, R.G.F.

AU - Bachem, C.W.B.

PY - 2005

Y1 - 2005

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AB - Potato tuber development has proven to be a valuable model system for studying underground sink organ formation. Research on this topic has led to the identification of many genes involved in this complex process and has aided in the unravelling of the mechanisms underlying starch synthesis. However, less attention has been paid to the biochemical pathways of other important metabolites or to the changing metabolic fluxes occurring during potato tuber development. In this paper, we describe the construction of a potato complementary DNA (cDNA) microarray specifically designed for genes involved in processes related to tuber development and tuber quality traits. We present expression profiles of 1315 cDNAs during tuber development where the predominant profiles were strong up- and down-regulation. Gene expression profiles showing transient increases or decreases were less abundantly represented and followed more moderate changes, mainly during tuber initiation. In addition to the confirmation of gene expression patterns during tuber development, many novel differentially expressed genes were identified and are considered as candidate genes for direct involvement in potato tuber development. A detailed analysis of starch metabolism genes provided a unique overview of expression changes during tuber development. Characteristic expression profiles were often clearly different between gene family members. A link between differential gene expression during tuber development and potato tissue specificity is described. This dataset provides a firm basis for the identification of key regulatory genes in a number of metabolic pathways that may provide researchers with new tools to achieve breeding goals for use in industrial applications.

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KW - phytochrome-b

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KW - photoperiod

KW - conversion

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